Sequencing Output Files

File Type	File Description, Location, and Name
Base call files	Each tile analyzed is included in a base call file, aggregated in one file for each lane, for each cycle. The aggregated file contains the base call and encoded quality score for every cluster for that lane. Data\Intensities\BaseCalls\L00[X]—Files are stored in one folder for each lane. [Cycle].bcl.bgzf, where [Cycle] represents the cycle number in four digits. Base call files are compressed using block gzip compression.
Base call index file	For each lane, a binary index file lists the original tile information in a pair of values for each tile, which are tile number and number of clusters for the tile. Base call index files are created the first time a base call file is created for that lane. Data\Intensities\BaseCalls\L00[X]—Files are stored in one folder for each lane. s_[Lane].bci
Cluster location files	For each tile, the XY coordinates for every cluster are aggregated into one cluster location file for each lane. Cluster location files are the result of template generation. Data\Intensities\L00[X]—Files are stored in one folder for each lane. s_[lane].locs
Filter files	The filter file specifies whether a cluster passed filters. Filter information is aggregated into one filter file for each lane and read. Filter files are generated at cycle 26 using 25 cycles of data. Data\Intensities\BaseCalls\L00[X]—Files are stored in one folder for each lane. s_[lane].filter
InterOp files	Binary reporting files used for Sequencing Analysis Viewer (SAV). InterOp files are updated throughout the run. InterOp folder
RTA configuration file	Created at the beginning of the run, the RTA configuration file lists settings for the run. <Run folder Name>, RTAConfiguration.xml
Run information file	Lists the run name, number of cycles in each read, whether the read is an indexed read, and the number of swaths and tiles on the flow cell. The run info file is created at the beginning of the run. <Run folder Name>, RunInfo.xml
Thumbnail files	A thumbnail image for each color channel (red and green) for tiles 1, 6, and 12 from all cameras, top and bottom surfaces, at every cycle during imaging. Thumbnail_Images\L00[X]\C[X.1]—Files are stored in one folder for each lane and one subfolder for each cycle. s_[lane]_[tile]_[channel].jpg—In the file name, the tile is represented with a five-digit number that indicates surface, swath, camera, and tile. For more information, refer to Tile Numbering and Thumbnail Image Naming.

Base call files

Each tile analyzed is included in a base call file, aggregated in one file for each lane, for each cycle. The aggregated file contains the base call and encoded quality score for every cluster for that lane.

Data\Intensities\BaseCalls\L00[X]—Files are stored in one folder for each lane.

[Cycle].bcl.bgzf, where [Cycle] represents the cycle number in four digits. Base call files are compressed using block gzip compression.

Base call index file

For each lane, a binary index file lists the original tile information in a pair of values for each tile, which are tile number and number of clusters for the tile.

Base call index files are created the first time a base call file is created for that lane.

Data\Intensities\BaseCalls\L00[X]—Files are stored in one folder for each lane.

s_[Lane].bci

Cluster location files

For each tile, the XY coordinates for every cluster are aggregated into one cluster location file for each lane. Cluster location files are the result of template generation.

Data\Intensities\L00[X]—Files are stored in one folder for each lane.

s_[lane].locs

Filter files

The filter file specifies whether a cluster passed filters. Filter information is aggregated into one filter file for each lane and read.

Filter files are generated at cycle 26 using 25 cycles of data.

Data\Intensities\BaseCalls\L00[X]—Files are stored in one folder for each lane.

s_[lane].filter

InterOp files

Binary reporting files used for Sequencing Analysis Viewer (SAV). InterOp files are updated throughout the run.

InterOp folder

RTA configuration file

Created at the beginning of the run, the RTA configuration file lists settings for the run.

<Run folder Name>, RTAConfiguration.xml

Run information file

Lists the run name, number of cycles in each read, whether the read is an indexed read, and the number of swaths and tiles on the flow cell. The run info file is created at the beginning of the run.

<Run folder Name>, RunInfo.xml

Thumbnail files

A thumbnail image for each color channel (red and green) for tiles 1, 6, and 12 from all cameras, top and bottom surfaces, at every cycle during imaging.

Thumbnail_Images\L00[X]\C[X.1]—Files are stored in one folder for each lane and one subfolder for each cycle.

s_[lane]_[tile]_[channel].jpg—In the file name, the tile is represented with a five-digit number that indicates surface, swath, camera, and tile. For more information, refer to Tile Numbering and Thumbnail Image Naming.